[Nicolas Novere comments on part of a recent proposal for BioPAX to
be presented tomorrow: http://mumble.net/~alanr/cshl/URICV.htm]
On Jun 19, 2006, at 5:45 AM, Nicolas Le Novere wrote:
Regarding this problem, we should team-up because we already did
it. We bumped into the same problems for quantitative modelling, and
decided to use the same systems of unique URIs. See:
Yes, the problem pops up everywhere. See recent threads on public-
semweb-lifesci
http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006May/
0042.html
http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006Jun/
0149.html
We are having a teleconference about this in (checks clock) 5
minutes. Details
Here http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/
2006-06-19_Conference_Call
Do consider joining the conversation.
There is also LSID to consider.
Do you have a specification of your web service available?
We should indeed all work together on this!
-Alan
Le Novère N., Finney A., Hucka M., Bhalla U., Campagne F., Collado-
Vides J., Crampin E., Halstead M., Klipp E., Mendes P., Nielsen P.,
Sauro H., Shapiro B., Snoep J.L., Spence H.D., Wanner B.L. (2005)
Minimum Information Requested In the Annotation of biochemical
Models (MIRIAM). Nature Biotechnology, 23: 1509-1515.
http://dx.doi.org/10.1038/nbt1156
The new version of SBML has a formal way of using those UIRs:
http://sbml.org/wiki/sbml-level-2-version-2.pdf
See section 6.
Since then, we have been developing a database to store those standard
URIs and all the related information (name, synonyms, URLs,
regular-expression to parse accession, associated documentation etc.)
We developed WebServices to access the database. Therefore when a tool
will parse an SBML file, it will be able to transform the URIs into
physical URLs etc. Conversely, a tool will be able to generate the
correct URI using the name of a resource and an accession.
The database is not publicly available yet, but we already use it for
BioModels Database purpose. Our plan is to release the whole lot by
the end of August. But we could put a demo online before that.
My suggestion is for BioPAX to use MIRIAM URIs. I see two great
advantages to that: 1) our aim being exactly the same, it would
eliminate some redundant work. 2) SBML and BioPAX constituents would
be annotated using the same URIs, making the conversion so easier.
What do-you think?
On Mon, 19 Jun 2006, Alan Ruttenberg wrote:
http://mumble.net/~alanr/cshl/URICV.htm
It's subject to change, but any comments or questions are
appreciated.
Many thanks to quick, late night, reviews by Andrea, Joanne,
Matthias and Emek.
Regards,
Alan
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--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10
1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)
689218676
http://www.ebi.ac.uk/~lenov AIM screen name:
nlenovere
